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Page 1
Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species.
Bradnam KR, Fass JN, Alexandrov A, Baranay P, Bechner M, Birol I, Boisvert S, Chapman JA, Chapuis G, Chikhi R, Chitsaz H, Chou WC, Corbeil J, Del Fabbro C, Docking TR, Durbin R, Earl D, Emrich S, Fedotov P, Fonseca NA, Ganapathy G, Gibbs RA, Gnerre S, Godzaridis E, Goldstein S, Haimel M, Hall G, Haussler D, Hiatt JB, Ho IY, Howard J, Hunt M, Jackman SD, Jaffe DB, Jarvis ED, Jiang H, Kazakov S, Kersey PJ, Kitzman JO, Knight JR, Koren S, Lam TW, Lavenier D, Laviolette F, Li Y, Li Z, Liu B, Liu Y, Luo R, Maccallum I, Macmanes MD, Maillet N, Melnikov S, Naquin D, Ning Z, Otto TD, Paten B, Paulo OS, Phillippy AM, Pina-Martins F, Place M, Przybylski D, Qin X, Qu C, Ribeiro FJ, Richards S, Rokhsar DS, Ruby JG, Scalabrin S, Schatz MC, Schwartz DC, Sergushichev A, Sharpe T, Shaw TI, Shendure J, Shi Y, Simpson JT, Song H, Tsarev F, Vezzi F, Vicedomini R, Vieira BM, Wang J, Worley KC, Yin S, Yiu SM, Yuan J, Zhang G, Zhang H, Zhou S, Korf IF. Bradnam KR, et al. Among authors: lavenier d. Gigascience. 2013 Jul 22;2(1):10. doi: 10.1186/2047-217X-2-10. Gigascience. 2013. PMID: 23870653 Free PMC article.
Assemblathon 1: a competitive assessment of de novo short read assembly methods.
Earl D, Bradnam K, St John J, Darling A, Lin D, Fass J, Yu HO, Buffalo V, Zerbino DR, Diekhans M, Nguyen N, Ariyaratne PN, Sung WK, Ning Z, Haimel M, Simpson JT, Fonseca NA, Birol İ, Docking TR, Ho IY, Rokhsar DS, Chikhi R, Lavenier D, Chapuis G, Naquin D, Maillet N, Schatz MC, Kelley DR, Phillippy AM, Koren S, Yang SP, Wu W, Chou WC, Srivastava A, Shaw TI, Ruby JG, Skewes-Cox P, Betegon M, Dimon MT, Solovyev V, Seledtsov I, Kosarev P, Vorobyev D, Ramirez-Gonzalez R, Leggett R, MacLean D, Xia F, Luo R, Li Z, Xie Y, Liu B, Gnerre S, MacCallum I, Przybylski D, Ribeiro FJ, Yin S, Sharpe T, Hall G, Kersey PJ, Durbin R, Jackman SD, Chapman JA, Huang X, DeRisi JL, Caccamo M, Li Y, Jaffe DB, Green RE, Haussler D, Korf I, Paten B. Earl D, et al. Among authors: lavenier d. Genome Res. 2011 Dec;21(12):2224-41. doi: 10.1101/gr.126599.111. Epub 2011 Sep 16. Genome Res. 2011. PMID: 21926179 Free PMC article.
Compareads: comparing huge metagenomic experiments.
Maillet N, Lemaitre C, Chikhi R, Lavenier D, Peterlongo P. Maillet N, et al. Among authors: lavenier d. BMC Bioinformatics. 2012;13 Suppl 19(Suppl 19):S10. doi: 10.1186/1471-2105-13-S19-S10. Epub 2012 Dec 19. BMC Bioinformatics. 2012. PMID: 23282463 Free PMC article.
DSK: k-mer counting with very low memory usage.
Rizk G, Lavenier D, Chikhi R. Rizk G, et al. Among authors: lavenier d. Bioinformatics. 2013 Mar 1;29(5):652-3. doi: 10.1093/bioinformatics/btt020. Epub 2013 Jan 16. Bioinformatics. 2013. PMID: 23325618 Free article.
GATB: Genome Assembly & Analysis Tool Box.
Drezen E, Rizk G, Chikhi R, Deltel C, Lemaitre C, Peterlongo P, Lavenier D. Drezen E, et al. Among authors: lavenier d. Bioinformatics. 2014 Oct 15;30(20):2959-61. doi: 10.1093/bioinformatics/btu406. Epub 2014 Jul 1. Bioinformatics. 2014. PMID: 24990603 Free PMC article.
Optimal neighborhood indexing for protein similarity search.
Peterlongo P, Noé L, Lavenier D, Nguyen VH, Kucherov G, Giraud M. Peterlongo P, et al. Among authors: lavenier d. BMC Bioinformatics. 2008 Dec 16;9:534. doi: 10.1186/1471-2105-9-534. BMC Bioinformatics. 2008. PMID: 19087280 Free PMC article.
Critical Assessment of Metagenome Interpretation-a benchmark of metagenomics software.
Sczyrba A, Hofmann P, Belmann P, Koslicki D, Janssen S, Dröge J, Gregor I, Majda S, Fiedler J, Dahms E, Bremges A, Fritz A, Garrido-Oter R, Jørgensen TS, Shapiro N, Blood PD, Gurevich A, Bai Y, Turaev D, DeMaere MZ, Chikhi R, Nagarajan N, Quince C, Meyer F, Balvočiūtė M, Hansen LH, Sørensen SJ, Chia BKH, Denis B, Froula JL, Wang Z, Egan R, Don Kang D, Cook JJ, Deltel C, Beckstette M, Lemaitre C, Peterlongo P, Rizk G, Lavenier D, Wu YW, Singer SW, Jain C, Strous M, Klingenberg H, Meinicke P, Barton MD, Lingner T, Lin HH, Liao YC, Silva GGZ, Cuevas DA, Edwards RA, Saha S, Piro VC, Renard BY, Pop M, Klenk HP, Göker M, Kyrpides NC, Woyke T, Vorholt JA, Schulze-Lefert P, Rubin EM, Darling AE, Rattei T, McHardy AC. Sczyrba A, et al. Among authors: lavenier d. Nat Methods. 2017 Nov;14(11):1063-1071. doi: 10.1038/nmeth.4458. Epub 2017 Oct 2. Nat Methods. 2017. PMID: 28967888 Free PMC article.
SVJedi: genotyping structural variations with long reads.
Lecompte L, Peterlongo P, Lavenier D, Lemaitre C. Lecompte L, et al. Among authors: lavenier d. Bioinformatics. 2020 Nov 1;36(17):4568-4575. doi: 10.1093/bioinformatics/btaa527. Bioinformatics. 2020. PMID: 32437523
29 results